Journal ArticleDOI
The stoichiometric interaction model for mesoscopic MD simulations of liquid-liquid phase separation.
TLDR
In this article , the stoichiometric interaction (SI) potential was proposed to model the valency of the interacting domains of a mixture of SH3 domains and proline-rich motifs.About:
This article is published in Biophysical Journal.The article was published on 2022-10-01. It has received 3 citations till now. The article focuses on the topics: Medicine & Valency.read more
Citations
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Journal ArticleDOI
Theory and Simulation of Multiphase Coexistence in Biomolecular Mixtures.
TL;DR: A review of recent advances in the prediction and computational design of biomolecular mixtures that phase-separate into many coexisting phases can be found in this article , where the authors describe progress in developing analytical theories and coarse-grained simulation models to predict multiphase condensates with the molecular detail required to make contact with biophysical experiments.
Journal ArticleDOI
Biophysics of biomolecular condensates.
A.A. Joshi,Samrat Mukhopadhyay +1 more
TL;DR: The formation of biomolecular condensates has emerged as a new biophysical principle for subcellular compartmentalization within cells to facilitate the spatiotemporal regulation of a multitude of complex biological reactions as mentioned in this paper .
Posted ContentDOI
Postsynaptic protein assembly in three- and two-dimensions studied by mesoscopic simulations
Risa Yamada,Shoji Takada +1 more
TL;DR: In this article , a mesoscopic model of protein-domain interactions in postsynaptic density (PSD) was constructed and comparative molecular simulations were performed to compare the phase behaviors in 3D and 2D systems.
References
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Journal ArticleDOI
Biomolecular condensates: organizers of cellular biochemistry
TL;DR: This work has shown that liquid–liquid phase separation driven by multivalent macromolecular interactions is an important organizing principle for biomolecular condensates and has proposed a physical framework for this organizing principle.
Journal ArticleDOI
Phase transitions in the assembly of multivalent signalling proteins
Pilong Li,Sudeep Banjade,Hui-Chun Cheng,Soyeon Kim,Baoyu Chen,Liang Guo,Marc C. Llaguno,Javoris Hollingsworth,David S. King,Salman F. Banani,Paul S. Russo,Qiu-Xing Jiang,B. Tracy Nixon,Michael K. Rosen +13 more
TL;DR: Interactions between diverse synthetic, multivalent macromolecules (including multi-domain proteins and RNA) produce sharp liquid–liquid-demixing phase separations, generating micrometre-sized liquid droplets in aqueous solution.
Journal ArticleDOI
Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels
Masato Kato,Tina W. Han,Shanhai Xie,Kevin Y. Shi,Xinlin Du,Leeju C. Wu,Hamid Mirzaei,Elizabeth J. Goldsmith,Jamie Longgood,Jimin Pei,Jimin Pei,Nick V. Grishin,Douglas E. Frantz,Jay W. Schneider,She Chen,Lin Li,Michael R. Sawaya,David Eisenberg,Robert Tycko,Steven L. McKnight +19 more
TL;DR: It is discovered that exposure of cell or tissue lysates to a biotinylated isoxazole (b-isox) chemical precipitated hundreds of RNA-binding proteins with significant overlap to the constituents of RNA granules, offering a framework for understanding the function of LC sequences as well as an organizing principle for cellular structures that are not membrane bound.
Journal ArticleDOI
Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins.
TL;DR: In this article, the physical properties of disordered linkers were used to determine the extent to which gelation of linear multivalent proteins is driven by phase separation, which is the biologically preferred mechanism for forming membraneless bodies.
Journal ArticleDOI
G3BP–Caprin1–USP10 complexes mediate stress granule condensation and associate with 40S subunits
Nancy Kedersha,Marc D. Panas,Christopher A. Achorn,Shawn M. Lyons,Sarah Tisdale,Tyler T. Hickman,Marshall P. Thomas,Judy Lieberman,Gerald M. McInerney,Pavel Ivanov,Pavel Ivanov,Paul A. Anderson +11 more
TL;DR: Stress granule condensation of translationally arrested mRNAs requires G3BP and requires its RGG region for SGC and for interactions with 40S ribosomal subunits.
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